Monthly Archives: August 2010

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There’s already been a lot of blogospheric discussion of the BBC’s recent declaration that “Darwin may have been wrong” based on a recently-published paleontology paper. I hadn’t paid it much attention, because while sloppy science journalism irritates me, it’s not quite in my wheelhouse, expertise-wise. Then I actually got around to reading the paper, and it turns out that it’s directly related to some of my own work—and the conclusion that led to the sensationalistic sub-headline doesn’t make any sense.

Coauthors Sahney, Benton, and Ferry analyze the fossil record of four-limbed vertebrates—tetrapods—to show that in general, as more species evolve, they also evolve to fill a wider variety of ecological roles [$a]. Ecological roles are here defined by combinations of body size, diet, and habitat. (Sahney et al estimate there are 207 such combinations possible, though only 75 are “occupied.”) That’s a straightforward and mostly unsurprising result—the number of tetrapod species increases as tetrapods evolve new ways to make a living. But then we get to the conclusions of the paper, and things get weird.Sahney et al. conclude that because diversification is associated with finding unoccupied ecological roles, competition is mostly unimportant in the diversification of tetrapods: “Given the unrestricted access tetrapods have to ecospace, perhaps there is little need for competitive interactions to shape diversification.” In other words, if diversification happens by finding ways to make a living that aren’t already occupied, competition isn’t important.

Except that the very reason species diversify following an ecological opportunity like the development of a new ecological role is the lack of competition the new role provides. As my coauthors and I documented in a recently published literature review, competition shapes the kind of diversification documented by Sahney et al. in two ways: first, by its absence following the evolution of a new lifestyle; then in spurring an adaptive radiation as new species evolve to partition up the newly-available “ecospace.”

What makes this doubly odd is that Sahney et al. refer to another kind of ecological opportunity, the extinction of competitors, as a good example of competition-driven diversification. But a central insight of the literature on ecological opportunity is that diversifying because a whole bunch of ecological roles have just opened up is not fundamentally different from diversifying after a new mutation makes a never-before-seen ecological role possible. Think of it like starting a new business: to avoid competition, you could either sell an existing product in a place where no one else sells that product, or you can invent a product no one else offers. Both approaches give you a market all to yourself, and both are defined by competition.

It’s hard for me to understand why Sahney et al. don’t make this conceptual connection—which, for what it’s worth, has its roots in The Origin of Species.

Major, embarrassing update, 2010.09.20: So it turns out that the Slate article from which I learned that Jefferson was the FAITH portrait was pretty much dead wrong. In fact the image is of Samuel Adams, and the source is the same painting in the Adams Wikipedia article. (Although, Shepard Fairey-ized, he still looks like Jefferson to me.) Jefferson makes so little sense for a portrait of FAITH that not even Glenn Beck is stupid enough to try and make him one. I’ve pulled the image from Flickr to prevent propagation of a false meme. Oy.

So there’s this guy who’s really popular with folks who hold political opinions mostly in opposition to mine. It’s come to my attention (probably late, I know) that he’s been waving around images of Thomas Jefferson, George Washington, and Benjamin Franklin, à la Shepard Fairey’s Obama posters, with the words “Faith,” “Hope,” and “Charity” appended to each, respectively. Now, I might quibble with “Hope” for Washington (what about “Courage?”) and “Charity” for Franklin (I’m sure Ben would’ve preferred “Thrift”), but I really take issue with assigning “Faith” to Jefferson. If you don’t know why this is both silly and (for a non-faith-inclined person such as myself) irritating, I have two words for you: Jefferson Bible.

So, with a little help from the wonderful open-source image software Inkscape, I fixed it.

It’s the hot new pigment this season. A just-discovered form of chlorophyll allows the algae that produce it to photosynthesize using infrared light. (Wired Science)

One, two, three … many? Studies of monkeys, babies, and chickens suggest that the ability to count small numbers is innate, and separate from the ability to count larger numbers. (The Thoughtful Animal)

Can you hear me now? On the Galapagos islands, marine iguanas listen for the alarm calls of mockingbirds to know if a predator is approaching. (The Thoughtful Animal)

I start another semester as Teaching Assistant for Mammalogy next week, so here’s David Attenborough discussing mammalian dentition, with reference to an ancient omnivore I’d never heard about up to now.

I just built my first course webpage, for the Mammalogy lab I’ll be leading for this semester’s teaching assistantship. It pulls together a bunch of resources I developed for the same lab last year—photos of lab specimens taken by students (thanks to a little extra credit for inducement) and Anki decks. Now I need to get started on the slides for my first week’s lecture …

Two of the most diverse groups of living things on Earth are flowering plants and the insects that make their living from flowering plants. Biologists have long thought that the almost incessant, intimate interactions between plants and plant-eating insects might be the evolutionary cause of each group’s spectacular diversity. On a smaller scale, this means that we’re interested in the reasons that specific insects and plants interact in the first place—what evolutionary trails leads one insect species to specialize on a single host while others eat pretty much any plant they land on.

A new study of one group of plant-eating insects suggests that the kind of interaction between insects and their host plants also determines how specific those interactions are. Examining a group of moths that, like the yucca moths I study, pollinate their host plant and then eat some of its seeds, the authors of the new study find that related, non-pollinating moths use more host plant species than the pollinators [$a]. I think it makes a particularly nice companion piece to my post about the evolutionary origins of yucca moths, because it provides an example of one or two other things biologists can deduce from phylogenies—and, as we’ll see, some things they can’t.

Epicephala: like a yucca moth without the snappy name

The moths in question are in the genus Epicephala, and they have an obligate pollination relationship with trees in the genus Glochidion, a diverse group of plant species found in southern Asia. That is, female moths carry pollen between Glochidion flowers in special mouthparts, deliberately apply pollen to the flower, and then lay eggs in the flower so that, when it develops into a fruit, her larvae can eat some of the seeds inside. Epicephala species are highly specialized, with most species only using one species of Glochidion [$a]. That’s a higher degree of specialization than what’s seen in yucca moths, in fact.

The family of which Epicephala is a member happens to include other moths that interact with Glochidion, but only as herbivores: species in the genera Caloptilia and Diphtheroptila, whose larvae all eat Glochidion leaves. Do these antagonistic moths use more, or fewer, species of the host plant than the mutualistic Epicephala? Kawakita and his coauthors set out to answer that question by reconstructing the phylogenies of Caloptilia and Diphtheroptila.Finding species in evolutionary trees

Most biologists agree that two groups of organisms are separate species if there is no gene flow between them. A consequence of genetic isolation between species is that, if they’re isolated long enough, they become monophyletic within phylogenies. That is, all the individuals within each species share a common ancestor that is not shared with any other species. You can see this by contrasting two monophyletic species (on the left in the figure below) with two groups that turn out to be paraphyletic—some individuals of the red species are more closely related to individuals of the blue species than to other individuals of their own species.

Monophyletic and paraphyletic groupings. Image by jby.

The reasoning behind this is a bit subtle. Paraphyletic groups might still be separate species—they just haven’t been isolated long enough to become monophyletic. As a good example, I’m a coauthor on a recent study that did this kind of analysis on non-pollinating “bogus” yucca moths that use three different yucca species. In that case, the moths were paraphyletic with respect to which yucca species they used, but more analysis showed that there is currently very little gene flow between moths using different hosts [PDF].

In the case of the Glochidion-using Caloptilia and Diphtheroptila, Kawakita et al. found something more complicated. Each genus broke up into several monophyletic groupings, or clades of genetically similar individuals—but in most cases each clade included moths collected from at least two different Glochidion species. Kawakita et al. note that the clades also correspond to differences in the moths’ wing coloration, larval feeding behavior, and genitalia, and conclude that each clade is a different species. That would mean that the two antagonist genera tend to use multiple host plants.

Interesting question, but is this the way to answer it?

Except I’m not sure I buy this usage of phylogenies to define species. Kawakita et al. have shown that within the clades they call species, the individuals all have very similar genetics, but only for the two commonly-used genetic markers from which the phylogenies are reconstructed. It’s not impossible that within each clade the moths might be adapted to individual host plant species, and reproductively isolated by that adaptation—and this could have happened recently enough that not many genetic differences would have built up in the two markers.

To really answer the question Kawakita et al. have posed would require a study of each clade in the two antagonist genera at a much finer scale. The question of how specialized Caloptilia and Diphtheroptila are hinges on how many species are in each genus, and that’s better addressed by examining population genetics, not ancient relationships among these genera.

Right now there’s a single page listing recent feed results from all these group blogs, and another devoted to science-y blog carnivals, but no independent blogs (ahem), and no particular way of sorting through the contents. It looks more like a starting point than a finished product, and that’s just fine—Bora and his co-founders Anton Zuiker and Dave Munger are still looking for input. Says Dave:

The site is really just an aggregator of aggregators. Everything you see on the front page is a feed from some other bundle of blogs. In a couple cases, we made our own bundles using Friendfeed. The site is flexible enough to add additional bundles as bloggers and publishers form new blogging communities. It’s not ideal — I think the ultimate science blog aggregator will allow users to view blog posts by topic, and perhaps have some way of identifying the best posts. But it’s flexible enough that with some input from the community, we might be able to shape it into something really special. Check it out, and let us know what you think.

As a blogger without a network, I’m naturally interested in seeing independent blogs added to the ScienceBlogging.org stream (although, as Bora points out, we’re already partially accounted for by including the Research Blogging feed). The large number of indy science bloggers would make this challenging, to say the least, but I think many of the issues are the same ones that show up, in smaller scale, on the new ScienceBlogging.org homepage—how to make it easy for a visitor to sift through a large number of posts to find writing by particular people, on particular topics, written in a particular time-frame.

Maybe what’s needed is an analogue to ResearchBlogging that aggregates all posts from member blogs and sifts them into topic-labeled feeds—but that’s a whole different class of infrastructure, and effort from member blogs, than what’s provided at the new site right now. Still, the value of a true one-stop shop for online science writing should be great enough to justify the effort. In the meantime, I’ve added a new bookmark, and I’ll be keeping an eye on ScienceBlogging.org.

A brand-new blog carnival promises to unleash the naughtier impulses of the science blogosphere which, let’s be frank, were never particularly tightly leashed to begin with. Except for the ones that are into that sort of thing.

Ahem.

Anyway, the inaugural edition of the Carnal Carnival is now online at A Blog Around the Clock, where host Bora Zivkovic called for any and all posts relating to poop, feces, dung, and/or excreta. The only shit-related question left unanswered in this fecund roundup is, shouldn’t they have saved this topic for Carnal Carnival #2?

First Ginsu salesman still millions of years away, though. Newly discovered bones bear scratch marks that could have been made by flaked stone cutting tools 3.4 million years ago—more than 800 thousand years earlier than previous evidence of such toolmaking by human ancestors. (Greg Laden’s Blog, Not Exactly Rocket Science)

I thought they said it had all magically disappeared? As much as 70% of the oil spilled by the now-plugged Deepwater Horizon well is still out there, somewhere. In fact, it’s probably suspended in the deep ocean, where microbes expected to break down oil may take months to finish it off. (Deep Sea News, Wired Science)

Being pecked to death never looked so unpleasant. Stress analysis of terror bird skulls suggest they killed prey by repeatedly stabbing it with the dagger-like tip of their beaks. (Not Exactly Rocket Science)

Is there an HVAC engineer in the house? We might be able to save bats from white-nose syndrome by heating their hibernation caves. (Wild Muse)

I would hope you don’t have to be as much of a news junkie as I am to know that, right now, tens of millions of people have just watched their lives—fields, homes, entire villages—wash away in Pakistan. (NASA has some astonishing before-and-after images.) For reasons political and logistical, aid is not arriving very fast where it’s most needed. So let me take this opportunity to suggest that my readers direct a contribution to Doctors Without Borders/Médicins Sans Frontières, which was on the scene pretty much from the start. I make a (very small) monthly contribution to MSF, which they like because it’s income they can count on—if you can, I’d suggest going that route.